Interpreting Results from FUMA - r2 values

[Avni Kaur]

Apologies for the confusion but I am little unsure what to make of my results  

From what I know, the Independent significant SNPs are independent from each other
at r2 < 0.6 and lead SNPs are  independent significant SNPs that are in LD with each other at r2 < 0.1

When I look into the ID.txt file to identify the r2 value of my independent sig SNPs which are the same as the lead SNPs. The values for the r2 value aren't <0.6 or < 0.1 E.g. For one my SNPs the r2 value is 0.678698. For another one I have a r2 value of 1. So I am little confused as to how FUMA identified the independent sig SNPs or lead SNPs?

Kind Regards,

Avni Kaur 

[d.p.wi...@vu.nl]

Hi, 

Do you mean in ld.txt? Can you share an example?

The lead SNPs are defined by clumping ind sig SNPs at r2 0.1, so all ind sig SNPs have r2<0.6 from each other, and lead SNPs have r2<0.1 from each other.

Cheers,

Doug

[Avni Kaur]

Hi Doug,

Thanks for getting back to me. Apologies for the late reply.

Yes this is in id.txt as well as the r2 column in SNPs.txt

I thought the r2 values should be low rather than high.  All the values in this column  are above 0.6/0.7

I also notice the r2 values = 1 are the lead SNPs/significant lead SNPs.

Kind Regards,

Avni